SAVAGEAU, M.A. (1976). Biochemical System Analysis: A Study of Function and Design in Molecular Biology (Addison -Wesley, New York). Home/Search Document Not in Database Summary Related Articles Check |
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A Symbolic Approach to Modeling Cellular - Behavior Bhubaneswar Mishra (Correct)
....of the underlying di erential algebraic system and the mathematical and computational problem they naturally lead to. 1.1 Outline 1. S systems: Section two gives a short biological introduction and then describes Savageau Voit approach to model bio chemical reactions based on S systems. See [11, 10]. 2. Canonical Forms: Section three provides a canonical description of an S system in terms of a system of di erential binomial equations and set of linear equality constraints. This formulation suggests that a biological system can always be described as a di erential system evolving on a ....
Savageau, M.A.: Biochemical System Analysis: A Study of Function and Design in Molecular Biology . Addison-Wesley, 1976.
Foundations of a Query and Simulation System for.. - Antoniotti, Park, .. (2003) (Correct)
....such traces are the result of simulating mathematical models of biochemical systems. Such models usually consist of relatively simple sets of di erential algebraic equations (DAE) alongside with their numerical solutions. e.g. the well known Generalized Mass Action systems (GMA) and S systems [1, 2, 3]. In this paper we reason about what are the necessary theoretical and pragmatic foundations for a query and simulation system capable of analyzing large amounts of trace data. To this end, we propose to combine in a novel way several well known tools from numerical analysis (approximation ....
....exibility and power, by integrating in a novel manner many commonly available tools from numerical analysis, symbolic computation, temporal logic, model checking, and visualization. We start by considering the the S systems models of biochemical processes developed mostly by Savageau and Voit [1, 2, 3], and extend them in order to facilitate their analysis. We name such extension XS system. The main innovation provided by an XS system consists in an automatonbased semantics of the temporal evolution of complex biochemical reactions presented as a set of DAE. Such automaton based semantics has ....
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M. A. Savageau. Biochemical System Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, 1976.
Inferring a System of Differential Equations for a Gene.. - Sakamoto, Iba (2001) (5 citations) (Correct)
....acquired system. system is given as follows: dX i dt = # i n # j=1 X g ij j # i n # j=1 X h ij j (i =1, 2, n) where X i is a state variable. The first term represents all influences that increase X i , whereas the second term represents all the influences that decrease X i [Savageau76]. The effectiveness of the LMS method. The rest of this paper is organized as follows. In Section 2, we describe the details of our method, i.e. how GP and LMS methods work in the course of evolution. Three examples of the target networks are used to examine the effectiveness of our method. ....
Savageau, M.A., Biochemical Systems analysis: a study of function and design in molecular biology, Addison-Wesley, Reading, 1976.
Algorithms for Inference of Genetic Networks (AIGNET) - Shoji Watanabe Yukihiro (1998) (Correct)
....to two different network models. One is a multi level digraph approach corresponding to a static Boolean network model, which mainly relies on the analysis of state changes of gene expression patterns resulting from deletion or forcible expression of one gene. The other is an S system [5] approach corresponding to a dynamic network model, which relies on the analysis of temporal responses of gene expression patterns to perturbations (e.g. heat shock, hormone stimulus) or internal changes (e.g. development) Individual approaches employed in AIGNET are described as follows. 2.1 ....
Savageau, M.A., Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology, Addison-Wesley, Reading, 1976.
Algorithms for Inference of Genetic Networks (AIGNET) - Shoji Watanabe Yukihiro (1998) (Correct)
....corresponding to two di#erent network models. One is a multi level digraph approach corresponding to a static Boolean network model, which mainly relies on the analysis of state changes of gene expression patterns resulting from deletion or forcible expression of one gene. The other is an S system [5] approach corresponding to a dynamic network model, which relies on the analysis of temporal responses of gene expression patterns to perturbations (e.g. heat shock, hormone stimulus) or internal changes (e.g. development) Individual approaches employed in AIGNET are described as follows. 2.1 ....
Savageau, M.A., Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology, Addison-Wesley, Reading, 1976.
AIGNET: Improvement of a System and Application to .. - Arikawa.. (Correct)
.... of Genetic Networ s) in which either of two completely di#erent networ models wor s independently [2] One model is a static Boolean networ model based on a multi level digraph approach which can treat a large number of expression data and the other is a dynamic networ model such as S system [3] which can infer the genetic networ including a group of interdependent genes. These two networ models wor in a cooperative manner in order to infer large scale genetic networ e#ectively. Using several sets of time course data corresponding to the deletion of one gene, we have been reconstructed a ....
Savageau M.A. Biochemical Systems analysis: a study of function and design in molecular biology Addison-Wesley Reading 1976.
Inferring a System of Differential Equations for a Gene.. - Sakamoto, Iba (2001) (5 citations) (Correct)
....form of Ssystem is given as follows: 0 21 3 465 )87 9; 3= 1 3 465 )2AB9; 3DCFE HG I JKI L L LMION P where )Q is a state variable. The first term represents all influences that increase )Q , whereas the second term represents all the influences that decrease )Q [Savageau76]. The robustness of the acquired system. The effectiveness of the LMS method. The rest of this paper is organized as follows. In Section 2, we describe the details of our method, i.e. how GP and LMS methods work in the course of evolution. Three examples of the target networks are used ....
Savageau, M.A., Biochemical Systems analysis: a study of function and design in molecular biology, Addison-Wesley, Reading, 1976.
After the Turing Machine - Kazic (1999) (Correct)
....and intimations in the literature. Analogies between networks of biochemical reactions, electrical circuits, and Boolean functions [2, 17, 23, 33, 39,40] graph theoretic approaches to reaction networks [14,33,34,38,48] and various quantitative approaches to the kinetics of large systems [8,15,49] are not new. John Ross and his colleagues have independently implemented one attempt with non nucleic acid based reactions (personal communication) and Michael Conrad has described some possible molecular computers more generally [9] 5.1 Towards a Theory of a CPC My group is attempting to ....
Savageau, M. A., 1976. Biochemical Systems Analysis: a Study of Function and Design in Molecular Biology. Addison-Wesley, Reading, MA.
OMICS A Journal of Integrative Biology - Volume Number Mary (Correct)
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SAVAGEAU, M.A. (1976). Biochemical System Analysis: A Study of Function and Design in Molecular Biology (Addison -Wesley, New York).
Layout Search of a Gene Regulatory Network for 3-D.. - Hosoyama, Nasimul, Iba (2003) (Correct)
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Savageau, M.A., Biochemical Systems analysis: a study of function and design in molecular biology, Addison Wesley Reading, 1976.
Some New Directions in Control Theory Inspired by Systems Biology - Sontag (2004) (Correct)
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Savageau, M.A.: `Biochemical Systems Analysis. A Study of Function and Design in Molecular Biology' (Addison-Wesley, Reading, MA, 1976).
Construction of Genetic Network Using Evolutionary Algorithm and .. - Shin, Iba (2003) (Correct)
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Savageau, M.A., Biochemical System Analysis: a Study of Function and Design in Molecular Biology, Addison-Wesley, Reading, MA, 1976.
Integrated System for Inference of Gene Expression Network - Nakatsui, Ueda, Okamoto (2003) (Correct)
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Savageau, M.A., Biochemical Systems Analysis: A study of function and design in molecular biology, Addison--Wesley, Reading, 1976.
A Sense of Life - Mishra, Raoul-SamDaruwala, Zhou.. (Correct)
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M.A. Savageau. Biochemical System Analysis: A Study of Function and Design in Molecular Biology . Addison-Wesley, 1976.
Simulating Large Biochemical and Biological Processes and.. - Antoniotti, al. (2002) (Correct)
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M. A. Savageau. Biochemical System Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, 1976.
Foundations of a Query and Simulation System for.. - Antoniotti, Park, .. (2003) (Correct)
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M.A. Savageau. Biochemical System Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, 1976.
From specific gene regulation to genomic networks: .. - Thieffry, Huerta, .. (1998) (2 citations) (Correct)
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Savageau MA (1976) Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Reading, MA: Addison-Wesley.
Development Of A System For The Inference Of Large Scale.. - Maki, Tominaga, Okamoto (2001) (5 citations) (Correct)
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M. A, Savageau, Biochemical Systems analysis: a study of function and design in molecular biology (Addison-Wesley, Reading), (1976).
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